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The atoms in the rock begin joined together as molecules, when heated these individual molecules become less tightly bonded together and hence, flow as a liquid.

Depending on the type of rock these molecules may reform into a different crystalline structure than they started (as happens when limestone turns to marble).

As for the individual atoms, the only thing that happens to them is their electrons speed up and jump up energy levels, just like any other heated atom.

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Q: What happens to atoms when rocks melt?
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